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BMA_plotting.Rmd
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BMA_plotting.Rmd
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---
title: "TITLE"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
df_print: paged
editor_options:
chunk_output_type: console
---
# Init
```{r}
#global options
options(
digits = 2,
contrasts = c("contr.treatment", "contr.treatment")
)
if (F) {
devtools::install_github("merliseclyde/BAS")
}
#packages
library(kirkegaard)
load_packages(
BAS,
BMA,
BMS,
patchwork,
readxl
)
#ggplot2
theme_set(theme_bw())
```
# Data
```{r}
#load SPI dataset
spi = readxl::read_xlsx("inst/extdata/SPI2019.xlsx", sheet = 2) %>%
df_legalize_names()
#impute it insofar as reasonable, drop the rest
spi_orig = spi
spi = spi %>%
miss_impute()
#filter whatever is left with missing data
spi = spi %>%
miss_filter()
#standardize everything for comparison
spi = spi %>%
df_standardize(exclude_range_01 = F)
```
# Examples
## General modeling code
```{r}
#make up some semi-plausible model
spi_model = str_glue("{names(spi)[34]} ~ {str_c(names(spi)[c(21:33, 37:40)], collapse = ' + ')}")
```
## BAS
```{r}
#fit a BAS model
spi_bas_fit = BAS::bas.lm(spi_model, data = spi)
spi_bas_fit
spi_bas_fit %>% summary()
(spi_bas_fit_coefs = spi_bas_fit %>% coef())
#test combined plot
spi_bas_fit_coefs %>%
GG_BMA()
```
## BMA
```{r}
#fit a BMA model
spi_bma_fit = BMA::bic.glm(as.formula(spi_model), data = spi, glm.family = "gaussian")
spi_bma_fit
spi_bma_fit %>%
GG_BMA()
```
## BMS
```{r}
#restyle the data since this package is annoying
spi_bms = spi[, formula.tools::get.vars(as.formula(spi_model))]
#fit a BMS model
spi_bms_fit = BMS::bms(spi_bms)
#coefs
spi_bms_fit_coefs = spi_bms_fit %>% coef()
spi_bms_fit %>%
GG_BMA()
```
## Made up results
Input a data frame with the following columns: term, PIP, mean, sd
```{r}
set.seed(1)
made_up = tibble(
term = LETTERS[1:10],
PIP = runif(10),
mean = rnorm(10, sd = .5),
sd = runif(10, .1, .5)
)
made_up %>%
GG_BMA()
```
# Meta
```{r}
write_sessioninfo()
#upload to OSF
#avoid uploading the data in case they freak out again
if (F) {
library(osfr)
#auth
osf_auth(readr::read_lines("~/.config/osf_token"))
#the project we will use
osf_proj = osf_retrieve_node("https://osf.io/XXX/")
#upload files
#overwrite existing (versioning)
osf_upload(osf_proj, conflicts = "overwrite",
path = c(
"figs",
"data",
"notebook.html",
"notebook.Rmd",
))
}
```